GrafGen
This is the development version of GrafGen; for the stable release version, see GrafGen.
Classification of Helicobacter Pylori Genomes
Bioconductor version: Development (3.24)
To classify Helicobacter pylori genomes according to genetic distance from nine reference populations. The nine reference populations are hpgpAfrica, hpgpAfrica-distant, hpgpAfroamerica, hpgpEuroamerica, hpgpMediterranea, hpgpEurope, hpgpEurasia, hpgpAsia, and hpgpAklavik86-like. The vertex populations are Africa, Europe and Asia.
Author: William Wheeler [aut, cre], Difei Wang [aut], Isaac Zhao [aut], Yumi Jin [aut], Charles Rabkin [aut]
Maintainer: William Wheeler <wheelerb at imsweb.com>
citation("GrafGen")):William Wheeler, Difei Wang, Isaac Zhao, Yumi Jin, Charles Rabkin. GrafGen: Classification of Helicobacter Pylori Genomes. doi:10.18129/B9.bioc.GrafGen, R package version 1.9.0, https://bioconductor.org/packages/GrafGen.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GrafGen")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GrafGen")| GrafGen: Classifying H. pylori genomes | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Genetics, GenomeAnnotation, Software |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.3.0) |
| Imports | stats, utils, graphics, ggplot2, plotly, scales, RColorBrewer, dplyr, grDevices, GenomicRanges, shiny, cowplot, ggpubr, stringr, rlang |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/wheelerb/GrafGen/issues |
See More
| Suggests | knitr, rmarkdown, RUnit, BiocManager, BiocGenerics, BiocStyle, devtools |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GrafGen_1.9.0.tar.gz |
| Windows Binary (x86_64) | GrafGen_1.9.0.zip |
| macOS Binary (big-sur-x86_64) | GrafGen_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | GrafGen_1.9.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GrafGen |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GrafGen |
| Package Short Url | https://bioconductor.org/packages/GrafGen/ |
| Package Downloads Report | Download Stats |